Identification of sources of resistance and comparative metabolomic profiling of resistant and susceptible chilli germplasm to Meloidogyne incognita Race 1

Root-knot nematode, Meloidogyne incognita Kofoid and White, 1919 is a major endoparasite that causes significant economic losses in several Solanaceous crops worldwide, including chilli (Capsicum annuum). In the present study, 66 accessions were screened for sources of resistance to M. incognita Race 1. The accessions EC399535 and EC402105 showed less than 10 number of galls and egg mass per root system [RKI:2 (1–10 galls or egg mass/ root system)] and identified as resistant accessions against M. incognita. Further, metabolic profiling analysis in the roots of resistant and susceptible (EC378632 and Arka Lohit) accessions exposed to M. incognita was carried out using gas chromatography-mass spectrometry (GC-MS). Non-targeted metabolic analysis detected 116 metabolites, which were further subjected to partial least squares-discriminant analysis (PLS-DA) with variable importance in projection (VIP) score to measure accumulation pattern in resistant and susceptible genotypes. VIP score revealed that 14 metabolites showed higher accumulation (> 1.5 VIP score) in resistant germplasm compared to susceptible germplasm. Specific metabolites viz., phytosterols, delta-tocopherol and squalene showed > 2.0 VIP score. Heatmap analysis differentiated metabolite abundance in each germplasm under M. incognita-infected and non-infected conditions. Dendrogram clustering analysis of metabolites data clearly separated resistant and susceptible accessions. The most significant metabolic pathways activated in M. incognita-resistance were phenylalanine metabolism (0.23529 impact), and sesquiterpenoid and triterpenoid biosynthesis (0.21622 impact) and alanine, aspartate and glutamate metabolism (0.19784 impact). This study provides valuable insights into compounds involved in defense activities against M. incognita. However, more research on the nematostatic or nematicidal activities of these metabolites including chemical inhibition or gene silencing of metabolites in plants is required for understanding the resistance mechanism and utilizing these metabolites as a biomarkers in resistance breeding programme.